ABSTRACTTritrichomonas murisis a flagellated protist isolated from the cecum of wild mice in the Czech Republic. This commensal protist has been shown previously to alter immune phenotypes in laboratory mice. Other trichomonads, previously referred to asTritrichomonas musculisandTritrichomonas rainier, also naturally colonize laboratory mice and cause immune alterations. This report formally describes two new trichomonads,Tritrichomonas musculusn. sp., andTritrichomonas casperin. sp., at the ultrastructural and molecular level. These two protists were isolated from laboratory mice, and were differentiated by their size and the structure of their undulating membrane and posterior flagellum. Analysis at the18S rRNAand trans-ITSgenetic loci supported their designation as distinct species, related toT. muris. To further assess the true extent of parabasalid diversity infecting laboratory mice, 135 mice were screened at the NIH using pan-parabasalid primers that amplify the trans-ITSregion. Forty-four percent of mice were positive for parabasalids, encompassing a total of 8 distinct sequence types.Tritrichomonas casperiandTrichomitus-like protists were dominant.T. musculusandT. rainierwere also detected, butT. muriswas not. Our work establishes a previously underappreciated diversity of commensal trichomonad protists that naturally colonize the enteric cavity of laboratory mice.